The gods in Sengoku Youko are whimsical and often demand a price for their assistance. While the mountain god waived her original price of a soul from the sibling pair (Jinka and Tama). I can't recall what the resolution of Shinsuke's assistance from the flower god (she was a big help for the fight against the cloud god in retrieving the injured). At the end of the series we see the flower god hanging around what is presumably his tombstone.
When Shinsuke goes off to find Yazen, Hanatora (the "flower goddess") claims she has a reservation for his soul, so we can pretty much assume that's what she got out of that deal. I don't think the manga ever tells us exactly how those godly characters take souls, or what they do with the souls they collect, but we know that Hanatora also had a claim on Ashikaga Yoshiteru's soul. In Yoshiteru's case, she only collected her "payment" at the time of his death (and later "forged" the Shogun's soul into the soul-sword she gave Senya). Considering Hanatora is pictured nearby Shinsuke's tombstone, as you mentioned, I'd say it's implied that "taking his soul after he died" was the price she asked of Shinsuke as well.